1S48

Crystal structure of RNA-dependent RNA polymerase construct 1 (residues 71-679) from BVDV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the RNA-dependent RNA polymerase from bovine viral diarrhea virus establishes the role of GTP in de novo initiation.

Choi, K.H.Groarke, J.M.Young, D.C.Kuhn, R.J.Smith, J.L.Pevear, D.C.Rossmann, M.G.

(2004) Proc.Natl.Acad.Sci.Usa 101: 4425-4430

  • DOI: 10.1073/pnas.0400660101
  • Primary Citation of Related Structures:  1S49, 1S4F

  • PubMed Abstract: 
  • The bovine viral diarrhea virus (BVDV) RNA-dependent RNA polymerase can initiate RNA replication by a de novo mechanism without a primer. The structure of BVDV polymerase, determined to 2.9-A resolution, contains a unique N-terminal domain, in additi ...

    The bovine viral diarrhea virus (BVDV) RNA-dependent RNA polymerase can initiate RNA replication by a de novo mechanism without a primer. The structure of BVDV polymerase, determined to 2.9-A resolution, contains a unique N-terminal domain, in addition to the fingers, palm, and thumb domains common to other polymerases. The structure of BVDV polymerase complexed with GTP, which is required for de novo (primer-independent) initiation, shows that GTP binds adjacent to the initiation NTP, suggesting that the GTP mimics a vestigial RNA product. Comparison of five monomers in two different crystal forms showed conformational changes in the fingertip region and in the thumb domain that may help to translocate the RNA template and product strands during elongation. The putative binding sites of previously reported BVDV inhibitors are also discussed.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-dependent RNA polymerase
A
609Bovine viral diarrhea virus (isolate NADL)EC: 3.6.1.15, 3.4.21.113, 3.4.22.-, 3.6.4.13, 2.7.7.48
Find proteins for P19711 (Bovine viral diarrhea virus (isolate NADL))
Go to UniProtKB:  P19711
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 
  • Space Group: P 62 2 2
Unit Cell:
Length (Å)Angle (°)
a = 205.727α = 90.00
b = 205.727β = 90.00
c = 99.597γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance